--- MITgcm/doc/tag-index	2012/08/07 22:24:00	1.1709
+++ MITgcm/doc/tag-index	2012/11/09 22:51:48	1.1765
@@ -1,27 +1,392 @@
-$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1709 2012/08/07 22:24:00 gforget Exp $
+$Header: /home/ubuntu/mnt/e9_copy/MITgcm/doc/tag-index,v 1.1765 2012/11/09 22:51:48 heimbach Exp $
 $Name:  $
 
     Notes on tags used in MITgcmUV
     ==============================
 
+o pkg/seaice:
+  - complete merge of ITD code into seaice_growth.F
+    from MITgcm_contrib/torge/itd/code/
+    no verification so far, but Torge Martin tested
+    "1-D test case and Beaufort set up;
+    deliver okay results after 1 model year."
+  - complete merge of SEAICE_SIZE.h into all relevant routines
+  - move computation of eta at Z-points into calc_viscosities
+    + introduce global field etaZ
+    + add different methods for computing etaZ, for now the old
+      method (simple averages of eta to Z-points) is hardwired
+    + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual, 
+      seaice_preconditioner
+  - simplify computations for SEAICE_ZETA_SMOOTHREG
+  - seaice_preconditioner: 
+    + replace one remaining press by pressLoc (mistake)
+    + adjust printing of residuals
+  - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
+    + add (SEAICE.h) and rename some counters (initiliased in 
+      seaice_init_fixed.F)
+    + add _BEGIN/END_MASTER (myThid)  around print statements
+    + print total number of iterations and failures over SEAICE_monFreq
+      interval to STDOUT
+  - move control over output-messages by fgmres to seaice_jfnk to save
+    some operations
+  - move resetting initial guess for fgmres outside of seaice_fgmres_driver
+    in order to make restarts with sol .ne. zero (fgmres with restarts)
+    (seaice_jfnk.F, seaice_fgmres.F)
+  - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
+    a serious convergence problem when open boundaries are involved
+o pkg/ggl90: fix computation of control volumes for the case of 
+  ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
+  up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
+o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
+o pkg/autodiff
+  - Add inAdMode switch for SEAICEuseDYNAMICS:
+    SEAICEuseDYNAMICSinAdMode 
+    (extend logic in ADAUTODIFF_INADMODE_SET)
+o pkg/seaice
+  - Step 1 of merging ice-thickness distribution (ITD) code from
+    MITgcm_contrib/torge/itd/ (author: Torge Martin)
+    The code implements concept laid out in Thorndike et al. (1975);
+    code is enabled via CPP flag SEAICE_ITD
+    nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
+    code is not complete yet!!
+  - SEAICE_SIZE.h now included in almost all seaice routines
+o verification (using seaice):
+  - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
+    global_ocean.cs32x15.seaice ; update results.
+  - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
+  - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
+    offline_exf_seaice (previously compiling B-grid).
+o pkg/exf:
+  - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
+    to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
+    forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
+o pkg/layers (adjust changes from Sept 19):
+  - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
+    this allows to remove "layers_maxNum" dimension from all layers arrays.
+o pkg/layers (adjust changes from Sept 19):
+  - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
+  - snap-shot extended to all type of layers (not just the 1rst type);
+  - remove layers variables when corresponding CPP option is undef.
+o pkg/layers:
+  - rename pkg/layers variable and add new output (layer exist & un-weighted
+    velocity in layer)
+o pkg/seaice:
+  - simplify (?) ocean-drag coefficent computations by using
+    the same routine in all three solvers (saves some code lines)
+  - remove global fields DRAGA and DRAGS from C-grid code and
+    declare them locally in lsr.F (the only place where they are
+    still used)
+  - update AD output of lab_sea.evp (very sensitive anyway).
+o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
+  (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
+  and SEAICEuseJFNK=.true. A few things to note:
+  - involves a FGMRES, that is parallel but very inefficient,
+    because of many scalar products (global sums) in the Gram-Schmidt
+    orthogonalization method. Needs to be replaced. Original code
+    from J.-F. Lemieux
+  - preconditioner for FGMRES is a stripped down version of LSOR
+  - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
+    preconditioner. For the preconditioner, the default is set to 10.
+  - Jacobian times vector is computed with finite differences
+  - marginally related to JFNK-solver: add a smooth regularization for
+    zeta with tanh that will improve convergence (Lemieux and Tremblay,
+    2009) for any implicit solver (not implemented for EVP because EVP
+    does not need this regularization in the first place). Define
+    SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
+o eesupp/src:
+  - check in genmake2 that intrinsic S/R flush is available.
+  - add S/R to flush IO unit (if intrinsic S/R flush is available)
+  - flush standard & error msg unit before MPI termination
+  - if debugMode, flush IO unit after printing msg
+o pkg/ctrl:
+  - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
+    to ctrl_set_unpack_xyz.
+
+checkpoint64 (2012/10/09)
+o pkg/shelfice
+  - in mom_fluxform.F, mom_vecinv.F:
+    CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
+    Bug fix KappaRU -> KappaRV
+    does not change verification/isomip but may change other setups
+    (presumably constant KappaRU=KappaRV)
+  - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
+o pkg/obcs:
+  - fixed some indexing bugs in obcs_seaice_sponge.F
+  - added obcs relaxation subroutines for HSALT and HSNOW
+  - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
+o pkg/seaice:
+  - add "multicategory" parameterization for snow in analogy to ice,
+    default is off for now.
+o pkg/obcs:
+  - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
+    see verification/seaice_obcs/input.seaiceSponge for example application.
+  - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
+    index setting by master-thread. This fix multi-threads Pb in previous modifs.
+o pkg/layers :
+  - add diagnostics to pkg/layers
+  - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
+    (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
+o pkg/generic_advdiff/gad_implicit_r.F :
+  - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
+o pkg/seaice/seaice_growth.F:
+  - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
+o pkg/obcs:
+  - change default setting of OBCS_UVICE_OLD from defined to undef;
+  - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
+    in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
+  - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
+  - change OB null index value (OB_indexNone) to -99 ; this fix the problem
+    with Southern & Western OB at a tile edge (at least in a simple set-up).
+o pkg/obcs:
+  - change settings of OB index in case OB coincides with tile edge (shared by
+    2 tiles), so that common OB location is registered by both tiles (instead of
+    only 1). However, for Southern and Western OB, index value = 0 is not
+    recognized as valid OB index (=default null value) and needs to be fixed.
+  - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
+  - new parameter "OB_indexNone" for null index value (for now, still zero)
+    to replace hard-coded null index value of zero.
+o pkg/exch2:
+  - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
+    always check buffer-size (but outside the loop); move checking for valid
+    index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
+    print each tile and point connection only if |W2_printMsg|>= 2 and 3.
+o pkg/ctrl (pack & unpack):
+  - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
+    (locally defined) for different variables (+ remove the variable-specific
+    file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
+    (to be extended to other local file names in ctrl.h).
+o pkg/flt:
+  - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
+o pkg/mdsio:
+  - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
+o tools/genmake2:
+  - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
+    (added by Alistair in version 1.51 for building without make depend);
+  - remove Header files list (H_SRC_FILES) from the dependence of targets
+     ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
+    place in version 1.23): this save going through staf when unrelated header
+    file has been modified.
+   Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
+    "make depend" step, still need to do "make links" before "make adtaf".
+o eesupp/src (+ few pkg src files) & genmake2:
+  - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
+  - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
+  - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
+     upper/lower case ; account for space between "#" and undef/define)
+o pkg/flt (with exch2):
+  - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
+  - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
+
+checkpoint63s (2012/09/05)
+o pkg/ecco:
+  - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
+  - add more relevant #ifdef ALLOW_SMOOTH ones.
+  - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
+o pkg/ctrl:
+  - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
+    ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
+  - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
+    doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
+    ctrlSmoothCorrel3D (new).
+    The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
+  - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
+  - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
+    controls when useAtmWind, and vice versa.
+  - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
+  - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
+      #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
+  - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
+      #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
+  - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
+    replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
+o pkg/smooth:
+  - remove un-necessary includes.
+  - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
+    Those CPP options were never defined, and not necessary.
+o model/src:
+  - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
+  - standard treatment of useSMOOTH.
+o pkg/autodiff:
+  - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
+    useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
+o pkg/exch2:
+  - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
+    + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
+  - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
+    and tiles to process mapping.
+  - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
+    moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
+    rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
+    from w2_eeboot.F to w2_readparms.F.
+o eesupp/src:
+  - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
+    ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
+    also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
+  - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
+    is defined (remove condition on usingMPI) to match cases where MPI_INIT
+    has been called.
+  - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
+  - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
+    (so that on 1 proc, get same myPid independently of usingMPI)
+  - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
+    useCubedSphereExchange with EXCH-1 (safer).
+  - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
+o pkg/ggl90:
+  - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
+    used in ALLOW_GGL90_SMOOTH code.
+o pkg/flt:
+  - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
+    floats at the Southern end of the domain).
+o eesupp/inc:
+  - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
+    but not used (and not to be used) anywhere, just for documentation.
+o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
+  - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
+    a) can damage previously written records in any other multi-record files.
+    b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
+o tools/genmake2:
+  - define variable MAKE within Makefile and use it in place of 'make';
+  - update AD_CONFIG.h (if needed) before building any of the executable
+    (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
+    and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
+  - always print usual warning comment 'this file is automatically generated'
+    from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
+o pkg/cheapaml:
+  - updated to correspond to the code used in accepted paper (Nico Wienders).
+o pkg/exf:
+    added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
+    ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
+    and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
+o pkg/exf, autodiff, ctrl, ecco and seaice:
+    remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
+o pkg/ctrl, ecco:
+    allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
+    Depending on useAtmWind, one is inactive, and the other is active (see
+    exf_getffields.F/exf_getsurfacefluxes.F).
+o tools/genmake2:
+  - improve error msg when failing in 2nd test of check_for_broken_Ff
+  - fix option '-makefile' short-name (-mf according to genmake2 -help)
+  - source local config file "genmake_local" just after processing the genmake2
+    command arguments (previously done before processing arg).
+o pkg/grdchk:
+  - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
+    to this routine from cost_final has been dropped in g_cost_final)
+  - improve printed information (more explicit msg, no longer using "print *,"
+     fix fcpertminus printed value).
+o model/src:
+  - move call to COST_INIT_VARIA out of packages_init_variables.F directly
+    into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
+    this prevents getting cost-funct reset in adinitialise_varia recomputations.
+o pkg/dic:
+  - move initialisation of "freefe" array from from dic_biotic_forcing.F to
+    fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
+o pkg/grdchk:
+  - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
+  - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
+o pkg/autodiff/ctrl/grdchk :
+  - attempt to sort out what works and what does not,
+    with regard to I/O, and to warn/stop accordingly.
+o pkg/grdchk:
+  - attempt to fix grdchk in the case of useSingleCpuIO.
+  - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
+   statements were moved from grdchk_main.F and into
+   grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
+  - a global sum is applied to record numbers icvrec/layer
+   out of grdchk_loc so that they be passed to I/O routines.
+o pkg/smooth:
+  - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
+    smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
+o verification/testreport:
+  - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
+  - can also use compressed (gzip) reference output file;
+  - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
+    to be easier to collect by testreport.
+  - update existing TLM output (half out-of-date by more than 3 yrs).
+  - report NETCDF & LAPACK settings (from genmake2) in output dir.
+  - report run-time in each individual summary (previously only for AD test);
+    for TLM test, add also TAF version.
+  - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
+
+checkpoint63r (2012/08/15)
+o tools/genmake2:
+  - fix Makefile for target ftlall (+ update files to clean after make ftlall)
+o pkg/ecco/ecco_cost_final.F :
+  - fix fc print statements (to stdout and costfunction0000) so
+    that the printed value is always after the global sum.
+o pkg/seaice/seaice_dynsolver.F :
+  - fix ice strength assymptote at SEAICE_area_max<1
+    (no change for the standard case of SEAICE_area_max=1)
+o some cleaning:
+  - pkg source files: ensure that all *.F files from each pkg included the
+    corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
+    only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
+    code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
+    includes;
+  - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
+  - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
+    is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
+    ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
+  - update option-file CPP_OPTIONS.h of all AD experiments:
+    * no longer include PACKAGES_CONFIG.h ;
+    * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
+    * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
+      including ECCO_CPPOPTIONS.h).
+o pkg/cost, pkg/ctrl, pkg/ecco option-file:
+  - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
+    separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
+    not necessary accurate).
+  - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
+    pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
+    deliberately break compilation (a remainder that it needs to be customized)
+  - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
+  - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
+  - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
+o tools/genamke2:
+  - check for lapack.
+o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
+  - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
+    jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
+    from both packages.
+  - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
+  - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
+  - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
+    of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
+o pkg/cost : add comments to explain special and/or untested setups.
+o pkg/exf:
+  - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
+    (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
+o verification/*/code_ad:
+  mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
+  - reccord when this file is included (define ECCO_CPPOPTIONS_H)
+  - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
+    allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
+o pkg/seaice :
+  - added possibility to change ice strength/PRESS0 relationship to
+    HEFF, according to the following run time parameters
+    SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
+    SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
+    SEAICEpresH0   :: HEFF threshold for ice strength            (m)
+o pkg/ggl90 :
+  - added run time flag mxlSurfFlag to include the code that ensure
+    mixing between first and second level (previously included as a comment)
 o verification/1D_ocean_ice_column/input_ad/data.autodiff :
-  - add test of newly added dumpAdByRec=T option where 
+  - add test of newly added dumpAdByRec=T option where
     we write all records to one file per variable.
 o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
   - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
     to check that this code is ok with taf and compiles in adjoint.
 o pkg/autodiff :
   - added run time param dumpAdByRec : ad dump format switch.
-   If true then write all records to one file per variable.
-   Else write one file per record (remains the default).
+    If true then write all records to one file per variable.
+    Else write one file per record (remains the default).
   - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
 o pkg/seaice:
  - Added SEAICEuseTILT run time switch : if set to
- false then omit the tilt term in seaice dynamics.
+   false then omit the tilt term in seaice dynamics.
  - Fix free drift calculation.
 o pkg/shelfice:
-  When initializing SHELFICEDragQuadratic, set default to be 
-  consistent with shiCdrag in case SHELFICEuseGammaFrict is used, 
+  When initializing SHELFICEDragQuadratic, set default to be
+  consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
   but retain option to set it independently
   (inconsistenty spotted by Veronique Dansereau)
 o eesupp/inc: